Understanding the thermodynamics and kinetics of biomolecule isomerization, such as protein folding, is a crucial task in order to determine the physical mechanisms of the process. To this aim the energy landscape paradigm has proved to be very successfull. However free-energy landscapes are usually untractable due to their high dimensionality and complexity. In order to overcome this problem the multidimensional free-energy landscape is mapped into a weighted graph. Here we present a network based analysis for the study of the system thermodynamics and kinetics of biomolecule isomerization without the use of arbitrarely chosen order parameters for the projection of the free-energy in 1 or 2 dimensions.